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When Red Sox owners John Henry and Tom Werner asked to meet with Terry Francona at Fenway Park Sept. 30, assistant general manager Ben Cherington was in the room along with Theo Epstein.

The topic that day was Francona’s future with the team. But clearly the Sox also were preparing for the departure of Epstein by putting Cherington in a position of greater authority.

When Epstein agreed to a five-year contract with the Cubs 12 days later, Cherington assumed control of baseball operations. His title becomes official Tuesday when the Sox introduce him as the new general manager.

Once the niceties of the news conference are complete, Cherington will have a long list of tasks that need to be accomplished.

The good news for Cherington is that he inherits a team that won 90 games and has an abundance of premium talent. But the Sox need a manager and have decisions to make on a number of key players. Cherington also faces the challenge of stitching up a clubhouse fabric that became torn during the team’s historic September collapse.

The new manager will play a key role in that effort. Cherington has been leading the search for Francona’s replacement, researching candidates to present to Henry, Werner, and team president Larry Lucchino. Once he is officially named GM, Cherington can bring those candidates in for interviews.

Because of the 10-day delay in Epstein’s transition to the Cubs, the search for a new manager had been on hold. It could be completed in a month.

The immediate decisions will come after the World Series when the team has to decide on the options it holds on shortstop Marco Scutaro ($6 million) and Dan Wheeler ($3 million).

Scutaro has a player option worth $3 million. The Sox originally signed him in the hope that Jose Iglesias would be ready to step in at shortstop by 2012. But Iglesias hit .235 at Triple A Pawtucket with a .554 OPS and appears to need more seasoning. That could increase the odds of Scutaro remaining with the team.

The Sox also have a brief window of exclusivity remaining with their in-house free agents: Erik Bedard, J.D. Drew, Jonathan Papelbon, Jason Varitek, and Tim Wakefield.

There is little chance the Sox would entertain keeping Drew, who is considering retirement. But Cherington will have to determine to what extent the Sox will try to retain the others.

Varitek and Wakefield have said they want to play next season and return to the Sox. But Varitek will be 40 in April and Wakefield is 45 and the Sox could simply decide that now is the right time to move on.

David Ortiz said last week that he hoped to remain with the Sox. The question is whether they will meet his price. Ortiz, who turns 36 in November, hit .309 with 29 home runs and 96 RBIs. Designated hitters have seen their value plummet on the open market in recent seasons.

Ortiz made $12.5 million this season. But given his age and lack of versatility, landing a comparable deal could be difficult.

Papelbon is sure to test the open market, which he has been looking forward to for years.

The future of righthander John Lackey is another thorny issue that Cherington will have to address.

Lackey is almost universally unpopular among the fan base, both for his poor pitching (a 5.26 earned run average in two seasons) and sour public disposition. The Sox surely would have to pick up much of the $45.75 million remaining on his contract to trade Lackey.

Lackey pitched much of this season with an elbow injury that could require surgery, something that obviously would keep the Sox from trading him.

The Sox have until Dec. 12 to decide whether to tender those players contract offers for 2012.

Cherington also has decisions to make beyond the roster. Henry has expressed concern over the team’s physical conditioning, and that is likely to mean a detailed review of the medical staff and its policies. The Sox also may need to reorganize the baseball operations staff in the wake of Epstein’s departure.

Epstein, who purchased a full-page advertisement in the Globe today to thank fans, will be introduced in Chicago Tuesday. But for the Red Sox, what Cherington has to say that day will be the big news.

Now that he’s the man in charge, the team can start the process of preparing for 2012 in earnest.